SMTL ID : 1tye.3 (2 other biounits)

Structural basis for allostery in integrins and binding of ligand-mimetic therapeutics to the platelet receptor for fibrinogen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- MAN- BMA: beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-MAN-BMA.1: 5 residues within 4Å: Chain A: R.281, M.285 Chain B: N.316, L.317, N.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.281, A:R.281

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: N.99, F.100, S.101 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain B: N.371, S.398, E.400 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.400 Hydrogen bonds: B:N.371, B:E.400

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.243, D.245, D.247, T.250, T.251, E.252 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.245, A:D.247, A:T.250, A:T.250, A:E.252 CA.4: 5 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.297, A:D.301, A:R.303, A:D.305, A:D.305 CA.5: 5 residues within 4Å: Chain A: D.365, D.367, D.369, Y.371, D.373 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.365, A:D.367, A:D.369, A:Y.371, A:D.373 CA.6: 5 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, D.434 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.426, A:D.428, A:Y.432, A:D.434, A:D.434 CA.11: 4 residues within 4Å: Chain B: S.123, D.126, D.127, D.251 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, B:D.251, H2O.2 CA.12: 7 residues within 4Å: Chain B: D.158, N.215, D.217, A.218, P.219, E.220 Ligands: CAC.9 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.158, B:D.217, B:D.217, B:P.219, B:E.220

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.9: 9 residues within 4Å: Chain B: S.121, Y.122, S.123, R.214, N.215, D.217, E.220 Ligands: MG.10, CA.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.121, B:Y.122, B:S.123, B:N.215 Water bridges: B:S.121, B:S.123

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain B: S.121, S.123, E.220 Ligands: CAC.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.121, B:S.123, B:E.220, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, T. et al., Structural basis for allostery in integrins and binding to fibrinogen-mimetic therapeutics. Nature (2004)

Release Date

2004-10-12

Peptides

Integrin alpha-IIb: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Integrin alpha-IIb

Integrin beta-3

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